Changes between Version 13 and Version 14 of SOPs/vcf_manipulation

Timestamp:

10/26/18 12:14:46 (6 years ago)

Author:

gbell

Comment:

--

SOPs/vcf_manipulation

@@ -101 +101 @@
 Extract fields from a VCF file to a TXT, tab separated format with [http://snpeff.sourceforge.net/SnpSift.html#Extract snpSift extractFields] function
 {{{
-# Extract chromosome, position, reference base(s), alternate bases(s), all the samples' DP4 (number of high-quality ref-fwd, ref-reverse, alt-fwd, alt-reverse bases):
-java -jar /nfs/BaRC/apps/snpEff/Version_4/SnpSift.jar extractFields - CHROM POS REF ALT GEN[*].DP4  foo.vcf > DP4.vcf
+# Extract chromosome, position, reference base(s), alternate bases(s), all the samples' ADF and ADR (number of high-quality ref-fwd, alt-fwd, ref-reverse, and alt-reverse bases):
+java -jar SnpSift.jar extractFields foo.vcf CHROM POS REF ALT "GEN[*].ADF" "GEN[*].ADR" > Foo.ADF.ADR.vcf
 
-# Similar command, but extract and split all PL fields
-java -jar /nfs/BaRC/apps/snpEff/Version_4/SnpSift.jar extractFields - CHROM POS REF ALT "GEN[*].PL[*]" foo.vcf > PL_values.vcf
+# Similar command, but extract and split all ADF and ADR fields
+java -jar SnpSift.jar extractFields foo.vcf CHROM POS REF ALT "GEN[*].ADF[*]" "GEN[*].ADR[*]" > Foo.ADF.ADR.split.vcf
 }}}